That's not how it works. If you have a clergy housing allowance, that amount is not reported on your W-2 anywhere (it could be reported in box 14 but that is just a memo field).
If your entire wages are designated as a housing allowance you should not get a W-2 at all, there is no way to issue one. (You can still file with Turbotax but must use a work-around.) If part of your wages are salary and part are designated as a housing allowance, you should get a W-2 with only the wages portion in box 1. Box 2 may or may not have federal tax withholding, and boxes 3-6 should be blank.
What is in boxes 1-6 of your W-2? If there is any figure in those boxes, then the church is not paying you correctly. You would need a corrected W-2 and the church would need to file amended form 941 or form 944 to correct the reporting of your wages and withholding.
